Diff in document structure when migrating from Azure CosmosDB to MongoDB

I'm trying to migrate a database from Azure CosmosDB to MongoDB Atlas using the official data migration tool. I've got the migration working in so far that the collections are being transfered, but the migrated documents have a different structure than the originals. It's nested in multiple objects. See examples below. I've tried researching the issue but haven't been able to find anything helpful.

What is the cause of this and is there a way for me to retain the original structure after the migration?

Original document structure in Azure CosmosDB:

{    _id: ObjectId("66666666666"),    user_id: "auth0|1234",    __v: 0}

Structure of migrated document in Atlas:

{    _id: ObjectId("66666666666"),    $t: 3,    $v: {        _id: Object,        user_id: {            $v: "auth0|1234"        }        __v: Object    }    id: "1234abc"}